p18
cell-loc
synapses
minor
params
smalldt
onsurface
migliore-1a
rallpack3
cwvclamp
vcsteps
rallpack1
smartrec
ivconv
ivconvm
mean-variance-iv-stoch
stochdet
channel-functions
stimtest
functest
migliore-pass
psd
cianmar30
mean-variance
rallpack2
rallpack3-stoch
rallpack3-stoch2
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multirec
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p1-f1-mean-variance
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singlecpt
synstim
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manychannels

stimtest (run.xml)

Current clamp stimulation profile read from a file, varying the stimulation scale factor

Total CPU time 0.1200 seconds; at 11:55:00 Thu 24 Sep 2009

CompartmentsStochastic
channels / cpmts
Continuous
channels / cpmts
Non Gated
channels / cpmts
time/mstimestep/msstim1:scaleFactorCPU Time / s
1590 / 00 / 00 / 025.00.01100 0.0400
1590 / 00 / 00 / 025.00.01200 0.0400
1590 / 00 / 00 / 025.00.01300 0.0400

Morphology: null

 

 

 

Predefined views

whole

enlarged

All files

ModelPreprocessedOutupt dataReference data etc
run.xml
membrane.xml
environment.xml
recording.xml
out-100.ppp
out-200.ppp
out-300.ppp
log.txt
out-100.sum
out-200.sum
out-300.sum
out-100.dat
out-100.txt
out-200.dat
out-200.txt
out-300.dat
out-300.txt
stim1.txt
NM1.swc
out-merged.txt

Model

Archive file of the complete model: stimtest.jar

run.xml

<PSICSRun timeStep="0.01ms" runTime="25ms" startPotential="-65mV" 
	environment="environment"
	properties="membrane"
	access="recording"
	stochThreshold="0">
	<MorphologySource format="swc" file="NM1b.swc"/>

	<StructureDiscretization baseElementSize="12um"/>

	<RunSet vary="stim1:scaleFactor" values="[100, 200, 300]"
		filepattern="out-$" merge="true"/>

<!-- nb this doesn't work - can't parse string arrays for values
	<RunSet vary="stim1:file" values="[stim1.txt, stim2.txt]"
		filepattern="out-$" merge="true"/>
 -->

	<info>Current clamp stimulation profile read from a file, varying the stimulation scale factor</info>


	<ViewConfig>
		<LineGraph width="500" height="400">
		<XAxis min="0" max="250" label="time / ms"/>
		<YAxis min="-80" max="60" label="potential / mV"/>

		<LineSet file="out-100.txt" color="red"/>
		<LineSet file="out-200.txt" color="orange"/>
		<LineSet file="out-300.txt" color="green"/>


		 <View id="whole" xmin="-10." xmax="50." ymin="-100." ymax="80."/>
		  <View id="enlarged" xmin="-10." xmax="50." ymin="-70." ymax="-50."/>
		</LineGraph>
	</ViewConfig>


</PSICSRun>

membrane.xml

<CellProperties id="membrane"
      cytoplasmResistivity="100ohm_cm"
      membraneCapacitance="1uF_per_cm2">



</CellProperties>

environment.xml

<CellEnvironment id="environment">
	<Ion id="Na" name="Sodium" reversalPotential="40mV"/>
	<Ion id="K" name="Potassium" reversalPotential="-80mV"/>
</CellEnvironment>

recording.xml

<Access id="recording" recordClamps="true">

	<CellLocation id="pA" path="10" rankBy="radius" sequenceFraction="1."/>

	

 
	<CellLocation id="pB" path="50" rankBy="radius" sequenceFraction="1."/>
	<CellLocation id="pC" path="120" rankBy="radius" sequenceIndex="0"/>

	<CellLocation id="pD" path="160" rankBy="radius" sequenceFraction="0.5"/>

	<VoltageClamp location="pA" hold="-75mV"/>

	<CurrentClamp location="pB" lineColor="red" hold="0.0nA">
	     <TimeSeries id="stim1" file="stim1.txt" timeUnit="1ms" valueUnit="0.01nA"
	     	scaleFactor="1.0"/>
	</CurrentClamp>



	<CurrentClamp location="pC" lineColor="red" hold="0.0nA">
	     <TimeSeries id="stim2" file="stim1.txt" column="2" timeUnit="1ms" valueUnit="0.01nA"
	     	scaleFactor="100.0"/>
	</CurrentClamp>
    <VoltageRecorder location="pD" lineColor="blue"/>
  




</Access>